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(-) Description

Title :  PSEUDOMONAS SERINE-CARBOXYL PROTEINASE COMPLEXED WITH THE INHIBITOR AIAF (THIS ENZYME RENAMED "SEDOLISIN" IN 2003)
 
Authors :  A. Wlodawer, M. Li, A. Gustchina, Z. Dauter, K. Uchida, H. Oyama, N. E. Gl B. M. Dunn, K. Oda
Date :  13 Nov 01  (Deposition) - 12 Dec 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine-Carboxyl Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Wlodawer, M. Li, A. Gustchina, Z. Dauter, K. Uchida, H. Oyama, N. E. Goldfarb, B. M. Dunn, K. Oda
Inhibitor Complexes Of The Pseudomonas Serine-Carboxyl Proteinase.
Biochemistry V. 40 15602 2001
PubMed-ID: 11747435  |  Reference-DOI: 10.1021/BI011817N

(-) Compounds

Molecule 1 - SERINE-CARBOXYL PROTEINASE
    Chains: A
    EC Number: 3.4.23.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 306
    Synonym: PSCP, PSEUDOMONAPEPSIN, PEPSTATIN-INSENSITIVE CARBOXYL PROTEINASE
 
Molecule 2 - AIAF PEPTIDE INHIBITOR
    Chains: B
    Engineered: YES
    Other Details: THE INHIBITOR WAS CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA1Ligand/IonCALCIUM ION
3GOL3Ligand/IonGLYCEROL
4PHL1Mod. Amino AcidL-PHENYLALANINOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:328 , VAL A:329 , GLY A:344 , GLY A:346 , ASP A:348 , HOH A:401BINDING SITE FOR RESIDUE CA A 3001
2AC2SOFTWAREASN A:9 , PHE A:48 , ASN A:52 , THR A:186 , LEU A:273 , TYR A:275 , LEU A:280 , HOH A:434 , HOH A:489 , HOH A:866BINDING SITE FOR RESIDUE GOL A 391
3AC3SOFTWAREGLY A:77 , HOH B:762 , HOH B:791 , HOH B:829 , HOH B:849 , ACE B:1001 , ILE B:1002 , ALA B:1003BINDING SITE FOR RESIDUE GOL B 392
4AC4SOFTWAREALA A:5 , ASN A:221 , GLU A:222 , HOH A:421 , HOH A:651BINDING SITE FOR RESIDUE GOL A 393
5AC5SOFTWAREGLU A:80 , SER A:133 , LEU A:134 , GLY A:135 , SER A:167 , GLY A:169 , ASP A:170 , GLU A:171 , ARG A:179 , SER A:190 , GLY A:285 , THR A:286 , SER A:287 , HOH A:637 , HOH A:851 , GOL B:392 , HOH B:708BINDING SITE FOR CHAIN B OF AIAF PEPTIDE INHIBITOR

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:137 -A:176

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:191 -Pro A:192
2Leu A:259 -Pro A:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KDV)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEDOLISINPS51695 Sedolisin domain profile.PICP_PSESR219-583  1A:4-368

(-) Exons   (0, 0)

(no "Exon" information available for 1KDV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:368
 aligned with PICP_PSESR | P42790 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:368
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577        
          PICP_PSESR    218 GTAKGHNPTEFPTIYDASSAPTAANTTVGIITIGGVSQTLQDLQQFTSANGLASVNTQTIQTGSSNGDYSDDQQGQGEWDLDSQSIVGSAGGAVQQLLFYMADQSASGNTGLTQAFNQAVSDNVAKVINVSLGWCEADANADGTLQAEDRIFATAAAQGQTFSVSSGDEGVYECNNRGYPDGSTYSVSWPASSPNVIAVGGTTLYTTSAGAYSNETVWNEGLDSNGKLWATGGGYSVYESKPSWQSVVSGTPGRRLLPDISFDAAQGTGALIYNYGQLQQIGGTSLASPIFVGLWARLQSANSNSLGFPAASFYSAISSTPSLVHDVKSGNNGYGGYGYNAGTGWDYPTGWGSLDIAKLSAYIRSNGF  585
               SCOP domains d1kdva_ A: Serine-carboxyl proteinase, SCP                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1kdvA00 A:3-370  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------Peptidase_S8-1kdvA01 A:29-363                                                                                                                                                                                                                                                                                                                  ------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.......eeeeeeeeeee..hhhhhhhhhhhhhhh........eee..........hhhhhhhhhhhhhhhhhhh...eeeeeeeee......hhhhhhhhhhhhhhh...eeee...eehhhhhhhhhhhhhhhhhhhhhhhhheeeee......................ee.......eeeeeeeeee.....eeeeee.eeee.....eee...eeeeeee.hhhhhhh.....eeee..eeee.hhhhheeeee....eee.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...ee...........................eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SEDOLISIN  PDB: A:4-368 UniProt: 219-583                                                                                                                                                                                                                                                                                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kdv A    3 GTAKGHNPTEFPTIYDASSAPTAANTTVGIITIGGVSQTLQDLQQFTSANGLASVNTQTIQTGSSNGDYSDDQQGQGEWDLDSQSIVGSAGGAVQQLLFYMADQSASGNTGLTQAFNQAVSDNVAKVINVSLGWCEADANADGTLQAEDRIFATAAAQGQTFSVSSGDEGVYECNNRGYPDGSTYSVSWPASSPNVIAVGGTTLYTTSAGAYSNETVWNEGLDSNGKLWATGGGYSVYESKPSWQSVVSGTPGRRLLPDISFDAAQGTGALIYNYGQLQQIGGTSLASPIFVGLWARLQSANSNSLGFPAASFYSAISSTPSLVHDVKSGNNGYGGYGYNAGTGWDYPTGWGSLDIAKLSAYIRSNGF  370
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        


Chain B from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                1kdv B 1001 xIAf 1004
                            |  |
                         1001-ACE
                            1004-PHL
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PICP_PSESR | P42790)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1kdv
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  3.4.23.33
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PICP_PSESR | P42790: 1ga1 1ga4 1ga6 1kdy 1kdz 1ke1 1ke2 1nlu

(-) Related Entries Specified in the PDB File

1ga1 PSCP WITH AN INHIBITOR BOUND IN THE P' SITE
1ga4 PSCP WITH AN INHIBITOR COVALENTLY BOUND
1ga6 NATIVE PSCP STRUCTURE
1kdy PSEUDOMONAS SERINE-CARBOXYL PROTEINASE COMPLEXED WITH THE INHIBITOR AIPF
1kdz PSEUDOMONAS SERINE-CARBOXYL PROTEINASE COMPLEXED WITH THE INHIBITOR TYROSTATIN
1ke1 PSEUDOMONAS SERINE-CARBOXYL PROTEINASE COMPLEXED WITH THE INHIBITOR PSEUDOTYROSTATIN
1ke2 PSEUDOMONAS SERINE-CARBOXYL PROTEINASE COMPLEXED WITH INHIBITOR CHYMOSTATIN